I'm curious to know what's the use case for using a separate indexes? You can connect to additional indexes by configuring the IClient implementation in code:
IClient yourOtherIndexClient = new Client(serviceUrl, indexName);
Before you consider this it's worth reading the official documentation on performance of the Client class: http://world.episerver.com/documentation/Items/Developers-Guide/EPiServer-Find/10/DotNET-Client-API/Client-class/
It's worth bearing in mind that it could be more difficult to use separate indexes if you want to index CMS and Commerce content.
Is it possible to configure EPiFind to use multiple indexes?
I know this is possible with Elasticsearch - but I don't see ay obvious way in the docs.